Spain has raked in more than €2.7bn (£2.29bn) in EU subsidies for its fishing industry over 12 years as part of a spending policy that Brussels admits has been a failure, according to data revealed today.

The figures suggest tens of millions have been spent subsidising vessels and practices exacerbating illegal fishing, increasing EU fleet over-capacity, and compounding overfishing in European waters.

Out of 27 countries in the EU, Spain got 48% of the subsidies dispensed, while the percentages for the other big fishing powers – France, Britain and Denmark – are only in single figures.

Two NGOs, the Pew Environment Group and EU Transparency, spent almost two years trying to obtain figures for the EU's Common Fisheries Policy (CFP) subsidies. A website – fishsubsidy.org – launched by them today analyses data obtained from the European Commission and member governments. Of €4.4bn in EU handouts to the fishing industry in 1994-2006, Spain got more than €2.7bn and Britain, where the Scottish fleets make up around 70% of the industry, was given €225m – a 12th of the Spanish total.

In the current EU budget period of 2007-13, Brussels is doling out a similar level of subsidies, €4.3bn – or €837m a year.

The figures show some of the biggest cash windfalls went to ships and firms notorious for their questionable operations. A huge Spanish trawler named by Greenpeace as the most egregious offender against vulnerable stocks of Mediterranean blue fin tuna enjoyed EU subsidies of more than €4m, and more from the Spanish government. Three vessels blacklisted by Greenpeace were given handouts believed to run into millions.

The CFP falls under the authority of Brussels and the commission, not national governments. The EU fisheries commissioner, Joe Borg, this year admitted the policy was a failure.

"The large majority of subsidies are spent on vessels fishing stock that are already overfished," said Marcus Knigge of Pew. The researchers found the subsidies policy was making over-capacity worse. In Spain, most of the funding went to building new boats, while in the other countries the bulk went towards scrapping vessels. At least seven vessels notionally scrapped under subsidy received further payments. The data indicates the names of the vessels, but not the actual beneficiaries of the payments, the owners and firms, since the official suppliers of the information refused to disclose that information.

"Vessels themselves are not the recipients of EU funds. It is the owner of the vessel who receives the funds," the researchers noted. "Record-keeping by members states is not good enough," said Jack Thurston of EU Transparency.